The Plant List is a working list of all known plant species. Version 1 aims to be comprehensive for species of Vascular plant (flowering plants, conifers, ferns and their allies) and of Bryophytes (mosses and liverworts).

Collaboration between the Royal Botanic Gardens, Kew and Missouri Botanical Garden enabled the creation of The Plant List by combining multiple checklist data sets held by these institutions and other collaborators.

The Plant List provides the Accepted Latin name for most species, with links to all Synonyms by which that species has been known. It also includes Unresolved names for which the contributing data sources did not contain sufficient evidence to decide whether they were Accepted or Synonyms.

Summary Statistics

The Plant List includes 1,040,426 scientific plant names of species rank. Of these 298,900 are accepted species names.

Bacteria Provide Example of One of Nature's First Immune Systems, Research Shows

ScienceDaily (Dec. 30, 2010) — Studying how bacteria incorporate foreign DNA from invading viruses into their own regulatory processes, Thomas Wood, professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University, is uncovering the secrets of one of nature's most primitive immune systems.

Single gram-negative Escherichia coli bacterium. Studying how bacteria incorporate foreign DNA from invading viruses into their own regulatory processes, Thomas Wood, professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University, is uncovering the secrets of one of nature's most primitive immune systems. (Credit: Janice Haney Carr)

His findings, which appear in Nature Communications, a multidisciplinary publication dedicated to research in all areas of the biological, physical and chemical sciences, shed light on how bacteria have throughout the course of millions of years developed resistance to antibiotics by co-opting the DNA of their natural enemies -- viruses.

The battle between bacteria and bacteria-eating viruses, Wood explains, has been going on for millions of years, with viruses attempting to replicate themselves by -- in one approach -- invading bacteria cells and integrating themselves into the chromosomes of the bacteria. When this happens a bacterium makes a copy of its chromosome, which includes the virus particle. The virus then can choose at a later time to replicate itself, killing the bacterium -- similar to a ticking time bomb, Wood says.

Received 26 May 2010 Accepted 25 November 2010 Published 21 December 2010

Phages are the most abundant entity in the biosphere and outnumber bacteria by a factor of 10. Phage DNA may also constitute 20% of bacterial genomes; however, its role is ill defined. Here, we explore the impact of cryptic prophages on cell physiology by precisely deleting all nine prophage elements (166 kbp) using Escherichia coli. We find that cryptic prophages contribute significantly to resistance to sub-lethal concentrations of quinolone and β-lactam antibiotics primarily through proteins that inhibit cell division (for example, KilR of rac and DicB of Qin). Moreover, the prophages are beneficial for withstanding osmotic, oxidative and acid stresses, for increasing growth, and for influencing biofilm formation. Prophage CPS-53 proteins YfdK, YfdO and YfdS enhanced resistance to oxidative stress, prophages e14, CPS-53 and CP4-57 increased resistance to acid, and e14 and rac proteins increased early biofilm formation. Therefore, cryptic prophages provide multiple benefits to the host for surviving adverse environmental conditions.

ScienceDaily (Dec. 30, 2010) — Researchers from George Washington University and the Smithsonian Institution have discovered evidence to debunk the theory that Neandertals' disappearance was caused in part by a deficient diet -- one that lacked variety and was overly reliant on meat. After discovering starch granules from plant food trapped in the dental calculus on 40-thousand-year-old Neandertal teeth, the scientists believe that Neandertals ate a wide variety of plants and included cooked grains as part of a more sophisticated, diverse diet similar to early modern humans.

"Neandertals are often portrayed as very backwards or primitive," said Amanda Henry, lead researcher and a post-doctoral researcher at GW. "Now we are beginning to understand that they had some quite advanced technologies and behaviors."

Dr. Henry made this discovery together with Alison Brooks, professor of anthropology and international affairs at GW, and Dolores Piperno, a GW research professor and senior scientist and curator of archaeobotany and South American archaeology at the Smithsonian National Museum of Natural History, Washington D.C., and Smithsonian Tropical Research Institute, Panama.

The discovery of starch granules in the calculus on Neandertal teeth provides direct evidence that they made sophisticated, thoughtful food choices and ate more nutrient-rich plants, for example date palms, legumes and grains such as barley. Until now, anthropologists have hypothesized that Neandertals were outlived by early modern humans due in part to the former's primitive, deficient diet, with some scientists arguing Neandertals' diets were specialized for meat-eating. As such, during major climate swings Neandertals could be outcompeted by early humans who incorporated diverse plant foods available in the local environment into their diets.

The nature and causes of the disappearance of Neanderthals and their apparent replacement by modern humans are subjects of considerable debate. Many researchers have proposed biologically or technologically mediated dietary differences between the two groups as one of the fundamental causes of Neanderthal disappearance. Some scenarios have focused on the apparent lack of plant foods in Neanderthal diets. Here we report direct evidence for Neanderthal consumption of a variety of plant foods, in the form of phytoliths and starch grains recovered from dental calculus of Neanderthal skeletons from Shanidar Cave, Iraq, and Spy Cave, Belgium. Some of the plants are typical of recent modern human diets, including date palms (Phoenix spp.), legumes, and grass seeds (Triticeae), whereas others are known to be edible but are not heavily used today. Many of the grass seed starches showed damage that is a distinctive marker of cooking. Our results indicate that in both warm eastern Mediterranean and cold northwestern European climates, and across their latitudinal range, Neanderthals made use of the diverse plant foods available in their local environment and transformed them into more easily digestible foodstuffs in part through cooking them, suggesting an overall sophistication in Neanderthal dietary regimes.

Footnotes

1To whom correspondence may be addressed. E-mail:ahenry@gwmail.gwu.edu or pipernod@si.edu.

Author contributions: A.G.H., A.S.B., and D.R.P. designed research; A.G.H. performed research; A.G.H. and D.R.P. analyzed data; and A.G.H., D.R.P., and A.S.B. wrote the paper.

What Triggers Mass Extinctions? Study Shows How Invasive Species Stop New Life

ScienceDaily (Dec. 30, 2010) — An influx of invasive species can stop the dominant natural process of new species formation and trigger mass extinction events, according to research results published December 29 in the journal PLoS ONE. The study of the collapse of Earth's marine life 378 to 375 million years ago suggests that the planet's current ecosystems, which are struggling with biodiversity loss, could meet a similar fate.

The ocean in Devonian times. A study of the collapse of Earth's marine life 378 to 375 million years ago suggests that the planet's current ecosystems, which are struggling with biodiversity loss, could meet a similar fate. (Credit: University of Michigan Museum of Paleontology)

Although Earth has experienced five major mass extinction events, the environmental crash during the Late Devonian was unlike any other in the planet's history. The actual number of extinctions wasn't higher than the natural rate of species loss, but very few new species arose.

"We refer to the Late Devonian as a mass extinction, but it was actually a biodiversity crisis," said Alycia Stigall, a scientist at Ohio University and author of the PLoS ONE paper.

"This research significantly contributes to our understanding of species invasions from a deep-time perspective," said Lisa Boush, program director in the National Science Foundation (NSF)'s Division of Earth Sciences, which funded the research.

Invasive Species and Biodiversity Crises: Testing the Link in the Late Devonian

Alycia L. Stigall*

Department of Geological Sciences and OHIO Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America

Abstract

During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied.Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity crisis.

Citation: Stigall AL (2010) Invasive Species and Biodiversity Crises: Testing the Link in the Late Devonian. PLoS ONE 5(12): e15584.

doi:10.1371/journal.pone.0015584

Editor: Anna Stepanova, Paleontological Institute RAS, United States of America

Funding: Funding was provided by the National Science Foundation (NSF) EAR-0922067, a grant from the American Chemical Society's Petroleum Research Fund, and Ohio University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The author has declared that no competing interests exist.

Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton ribonucleoprotein (RNP) complex comprised of five snRNPs and numerous proteins. Intricate RNA-RNA and RNP networks, which serve to align the reactive groups of the pre-mRNA for catalysis, are formed and repeatedly rearranged during spliceosome assembly and catalysis. Both the conformation and composition of the spliceosome are highly dynamic, affording the splicing machinery its accuracy and flexibility, and these remarkable dynamics are largely conserved between yeast and metazoans. Because of its dynamic and complex nature, obtaining structural information about the spliceosome represents a major challenge. Electron microscopy has revealed the general morphology of several spliceosomal complexes and their snRNP subunits, and also the spatial arrangement of some of their components. X-ray and NMR studies have provided high resolution structure information about spliceosomal proteins alone or complexed with one or more binding partners. The extensive interplay of RNA and proteins in aligning the pre-mRNA's reactive groups, and the presence of both RNA and protein at the core of the splicing machinery, suggest that the spliceosome is an RNP enzyme. However, elucidation of the precise nature of the spliceosome's active site, awaits the generation of a high-resolution structure of its RNP core.

Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK. gabriel.marais@ed.ac.uk

Abstract

Classical genetic studies show that gene conversion can favour some alleles over others. Molecular experiments suggest that gene conversion could favour GC over AT basepairs, leading to the concept of biased gene conversion towards GC (BGC(GC)). The expected consequence of such a process is the GC-enrichment of DNA sequences under gene conversion. Recent genomic work suggests that BGC(GC) affects the base composition of yeast, invertebrate and mammalian genomes. Hypotheses for the mechanisms and evolutionary origin of such a strange phenomenon have been proposed. Most BGC(GC) events probably occur during meiosis, which has implications for our understanding of the evolution of sex and recombination.

Specialists and collectors around the world have long decried the flood of sham fossils pouring out of China. But Science has learned that many composites and fakes are now finding their way into Chinese museums, especially local museums. One paleontologist estimates that more than 80% of marine reptile specimens now on display in Chinese museums have been "altered or artificially combined to varying degrees." One consequence of the fakery is an erosion of trust in museums, which are supposed to enlighten—not con—the public. Scholars, too, pay a price: They waste time sifting authentic specimens from counterfeit chaff. And a genuine blockbuster fossil can be destroyed by attempts to enhance its appeal.

Because solar energy is available in large excess relative to current rates of energy consumption, effective conversion of this renewable yet intermittent resource into a transportable and dispatchable chemical fuel may ensure the goal of a sustainable energy future. However, low conversion efficiencies, particularly with CO2 reduction, as well as utilization of precious materials have limited the practical generation of solar fuels. By using a solar cavity-receiver reactor, we combined the oxygen uptake and release capacity of cerium oxide and facile catalysis at elevated temperatures to thermochemically dissociate CO2 and H2O, yielding CO and H2, respectively. Stable and rapid generation of fuel was demonstrated over 500 cycles. Solar-to-fuel efficiencies of 0.7 to 0.8% were achieved and shown to be largely limited by the system scale and design rather than by chemistry.

domingo, dezembro 26, 2010

Normally, information from scientific discoveries is funnelled into the development of engineered products that benefit humanity.

But recently a strange turnabout in the flow of practical information has occurred.

Concepts from the field of engineering have been found extremely useful in areas of science.

From the very large aspects of the universe (i.e. big bang cosmology and galactic and stellar evolution) to the very small aspects (i.e. the fitness of the chemical elements and the coding of DNA for life), the cosmos is so readily and profitably reverse-engineered by scientists and engineers as to make a compelling argument that it was engineered in the first place.

The linking of extraordinarily complex, but stable functional structures with the production of value provides the strong impression of a calculating intentionality, which is able to operate in a transcendent fashion.

The most coherent view of the universe is that of a system of subsystems that efficiently interact to prepare for, develop, and support advanced life, subject to various physical constraints.

The quest for understanding our universe as a whole benefits from the integration of knowledge from all areas of study, including those that consider questions of purpose, such as design engineering.

The synthesis of this knowledge that provides the most satisfying answers regarding human experience is one that admits the recognition of purpose and the existence of an (as yet, not-wellunderstood) engineering influence.

Keywords:

cosmology, reverse-engineering, anthropic principle, engineering.

1 Introduction:

Throughout the ages, many great minds have expressed a profound appreciation for the incredible ingenuity of natural systems.

Edited* by Leslie Greengard, New York University, New York, NY, and approved November 12, 2010 (received for review June 25, 2010)

Abstract

Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions—lists of the most important players and the pairwise interactions between them. Both for large networks (in which statistical analysis is often framed in terms of the abundance of repeated small subgraphs) and for small networks which can be analyzed in greater detail (or even synthesized in vivo and subjected to experiment), revealing the relationship between the topology of small subgraphs and their biological function has been a central goal. We here seek to pose this revelation as a statistical task, illustrated using a particular setup which has been constructed experimentally and for which parameterized models of transcriptional regulation have been studied extensively.The question “how does function follow form” is here mathematized by identifying which topological attributes correlate with the diverse possible information-processing tasks which a transcriptional regulatory network can realize. The resulting method reveals one form-function relationship which had earlier been predicted based on analytic results, and reveals a second for which we can provide an analytic interpretation. Resulting source code is distributed via http://formfunction.sourceforge.net.